An alliance of immigration and civil rights organisations have filed a complaint to the Department of Homeland Security’s inspector general on behalf of more than 100 unaccompanied migrant children, some as young as five, alleging abuse by US Customs and Border Protection, in a document which they say reflects a “humanitarian crisis” at the border.

The groups, who have urged the DHS to investigate the allegations, say the documented reports reflect “widespread and systematic” abuse of such children in border agency custody, and warned that the crisis is compounded by the recent surge in unaccompanied migrant minors to the US.

The coalition, which includes the National Immigrant Justice Centre, Americans for Immigrant Justice (AIJ) and the ACLU border litigation project, among others, says the majority of the 116 children covered in the complaint, each of whom reported experiencing abuse and mistreatment while in CBP custody, came into the US because of violence in their home countries. The groups, who have filed similar complaints in the past, pointed to a lack of effective oversight and transparency at the agency.

“Border Patrol agents are committing appalling abuses of children all along the border,” said Ashley Huebner, managing attorney of the Immigrant Children’s Protection Project at the National Immigrant Justice Center. “Even worse, Border Patrol has been committing these abuses for years, and our organizations have notified the agency numerous times, yet nothing has changed. The recent increase in arrivals of young people at the border makes it especially urgent that CBP ensure all children in their custody are treated safely and humanely.”

Erika Pinheiro, directing attorney for community education programs at Esperanza Immigrant Rights Project, who interviewed more than 90% of the children in the complaint, said she considered their experiences representative of more than 1,000 interviews conducted. She said she had no way of corroborating the reports but said that many of the children's stories were similar. For instance, many of them spoke of the border agents telling them they hoped their planes they were travelling in would crash.

The groups said they intended to file litigation but were keen to draw attention to the issue immediately because of the urgency of the situation.

The alleged abuses, reported from approximately March to May 2014, paint a consistent picture of widespread mistreatment, the groups said, and were representative of of the treatment meted out to “thousands” of unaccompanied children: a lack of basic human requirements such as beds, food and water; prolonged detention in squalid conditions; and verbal, sexual and physical abuse.

One in four of the 116 children reported physical and sexual abuse, including one teenager who said she was raped by a CBP officer. More than half said they were denied medical care, including two young mothers whose infants became sick while detained in freezing temperatures. More than half also reported verbal abuse, including racial and sexually charged comments and death threats. About 70% of the 116 children reported being held beyond the legally mandated 72-hour period, the groups said. Many reported being painfully shackled, including two pregnant women who complained that they had been subjected to three-point shackles, which hurt their abdomens.

Reports of such abuses have been documented for at least a decade, the groups said, but no reforms have been implemented and agents are rarely held to account. For instance, the AIC found recently that 97% of the 809 abuse complaints – 60% of which involved abuse of migrant children – filed against Border Patrol agents between January 2009 and January 2012 resulted in the classification "no action taken".

The interviewed children, whose names were removed from the public report but given to DHS so it could investigate, included a seven-year-old boy with severe developmental disabilities who was suffering from malnourishment and weighed only 25lbs. He was held in CBP custody without medical treatment. He was eventually hospitalised and underwent emergency surgery.

“Children are fleeing untenable conditions in their home countries, including pervasive violence and persecution, and are often re-victimized in transit to the United States,” said Joseph Anderson, the director of litigation for Americans for Immigrant Justice. “We need to ensure that these children are treated with dignity and respect and afforded all applicable legal protections while they are in US custody.”

The complaint called for a prompt, thorough and public investigation of each of the allegations, and the punishment of individual officers guilty of unlawful or improper conduct.

It also recommended a series of reforms, including the creation of an independent CBP oversight body, binding and enforceable short-term detention standards, timely investigations of abuse, the publication of such investigations and accountability for officers.

In a statement issued on Wednesday, CBP said it "strives to protect unaccompanied children with special procedures and safeguards". "Mistreatment or misconduct is not tolerated," it said.

The statement cited the "overwhelming numbers" of unaccompanied children crossing the border. Still, CBP claimed it "does everything within its power" to process these children within 72 hours to the Department of Health and Human Services, and said, "Patrol agents have taken extraordinary measures to care for these children while in custody and to maintain security in overcrowded facilities".

The head of internal affairs for CBP, James Tomsheck, was removed from his post on Monday amid concern he did not thoroughly investigate hundreds of allegations of abuse and use of force by border patrol agents.